Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/scGraphVerse
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo2 Linux (Ubuntu 24.04.3 LTS)/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo2 Summary

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Package: scGraphVerse
Version: 0.99.3
RVersion: 4.5
BiocVersion: 3.22
BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scGraphVerse
BuildTime: 8 minutes 3.99 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: scGraphVerse_20250825185456
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scGraphVerse. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo2 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file scGraphVerse/DESCRIPTION ... OK
* preparing scGraphVerse:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building case_study.Rmd using rmarkdown
trying URL 'https://stringdb-downloads.org/download/protein.aliases.v11.5/9606.protein.aliases.v11.5.txt.gz'
Content type 'application/octet-stream' length 21726816 bytes (20.7 MB)
==================================================
downloaded 20.7 MB

trying URL 'https://stringdb-downloads.org/download/protein.info.v11.5/9606.protein.info.v11.5.txt.gz'
Content type 'application/octet-stream' length 1901833 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

--- finished re-building case_study.Rmd

--- re-building simulation_study.Rmd using rmarkdown

Quitting from simulation_study.Rmd:355-357 [sessioninfo]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `x[["Version"]]`:
! subscript out of bounds
---
Backtrace:
     
  1. tools::buildVignettes(dir = ".", tangle = TRUE)
  2.   base::tryCatch(...)
  3.    base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.      base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5.        base (local) doTryCatch(return(expr), name, parentenv, handler)
  6.   engine$weave(file, quiet = quiet, encoding = enc)
  7.     knitr:::vweave_rmarkdown(...)
  8.       rmarkdown::render(...)
  9.         knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10.           knitr:::process_file(text, output)
 11.             xfun:::handle_error(...)
 12.             base::withCallingHandlers(...)
 13.             knitr:::process_group(group)
 14.               knitr:::call_block(x)
 15.                 knitr:::block_exec(params)
 16.                   knitr:::eng_r(options)
 17.                     knitr:::in_input_dir(...)
 18.                      knitr:::in_dir(input_dir(), expr)
 19.                     knitr (local) evaluate(...)
 20.                       evaluate::evaluate(...)
 21.                         base::withRestarts(...)
 22.                          base (local) withRestartList(expr, restarts)
 23.                            base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 24.                             base (local) doWithOneRestart(return(expr), restart)
 25.                            base (local) withRestartList(expr, restarts[-nr])
 26.                              base (local) withOneRestart(expr, restarts[[1L]])
 27.                                base (local) doWithOneRestart(return(expr), restart)
 28.                         evaluate:::with_handlers(...)
 29.                          base::eval(call)
 30.                           base::eval(call)
 31.                          base::withCallingHandlers(...)
 32.                         watcher$print_value(ev$value, ev$visible, envir)
 33.                           base::withVisible(handle_value(handler, value, visible, envir))
 34.                           evaluate:::handle_value(handler, value, visible, envir)
 35.                             handler$value(value, visible)
 36.                               knitr (local) fun(x, options = options)
 37.                                 base::withVisible(knit_print(x, ...))
 38.                                 knitr::knit_print(x, ...)
 39.                                 knitr:::knit_print.default(x, ...)
 40.                                   knitr::normal_print(x)
 41.                                     base::print(x)
 42.                                     utils:::print.sessionInfo(x)
 43.                                       base::print(mkLabel(x, "loadedOnly"), quote = FALSE, ...)
 44.                                       utils (local) mkLabel(x, "loadedOnly")
 45.                                         base::sapply(L[[n]], function(x) x[["Version"]])
 46.                                           base::lapply(X = X, FUN = FUN, ...)
 47.                                             utils (local) FUN(X[[i]], ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building simulation_study.Rmd

SUMMARY: processing the following file failed:
  simulation_study.Rmd

Error: Vignette re-building failed.
Execution halted

nebbiolo2 CHECK output

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nebbiolo2 BUILD BIN output
 
                    			
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